Research workbench
Fab fragment of 5G6 in complex with epitope peptide
Analyse Fab fragment of 5G6 in complex with epitope peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4YR6
- Type
- protein
- Length
- 871 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.38
- Source
- Mus musculus; SYNTHETIC CONSTRUCT
- Molecule
- heavy chain of 5G6; light chain of 5G6; ACE-lys-leu-arg-gly-val-leu-gln-gly-his-leu
- Pockets
- 4 · best druggability 0.83
Structure
x-ray diffraction · resolution 2.38 · 5 distinct chains · 7% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | heavy chain of 5G6 | protein | 215 | 8% helix, 55% strand | — |
| B | light chain of 5G6 | protein | 212 | 7% helix, 51% strand | — |
| C, F | ACE-lys-leu-arg-gly-val-leu-gln-gly-his-leu | protein | 10 | 30% helix, 0% strand | — |
| D | heavy chain of 5G6 | protein | 213 | 8% helix, 55% strand | — |
| E | light chain of 5G6 | protein | 211 | 5% helix, 51% strand | — |
Ligands and binding sites
- GOL · Glycerol · additive · 2 copies · chains B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 833 | 0.83 | 0.85 | 109 | empty |
| 2 | 244 | 0.56 | 0.78 | 38 | empty |
| 3 | 104 | 0.36 | 0.74 | 24 | empty |
| 4 | 85 | 0.34 | 0.74 | 19 | empty |
Interfaces
10 interfaces between chains.
- A–B · 1708 Ų buried · 12 hydrogen bonds · protein-protein
- D–E · 1704 Ų buried · 12 hydrogen bonds · protein-protein
- A–E · 444 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 382 Ų buried · 6 hydrogen bonds · protein-protein
- D–F · 377 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 4YR6 · Fab fragment of 5G6 in complex with epitope peptide · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 4YR6 · PDBe 4YR6
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